Biology subjects

Chong, A.

Publications and source records attributed to Chong, A..

9 recordsLinked to original sources

bioRxiv2025

The mycobacterial ATP burst is a lysis artifact and serves as an assay for drug-induced cell wall damage

Antibiotics targeting the mycobacterial cell wall are a cornerstone of tuberculosis treatment. Understanding how these drugs facilitate bacterial killing has important implications for identifying novel therapeutic targets and optimizing drug combinations. Previous studies on mycobacteria using the BacTiter-Glo luminescence assay have reported increased ATP levels after treatment with cell wall inhibitors such as isoniazid, a phenomenon referred to as an ATP burst. This phenomenon has been proposed to contribute to drug-induced killing. In this study, we demonstrate that the ATP burst is not a biological response but rather an experimental artifact resulting from enhanced cell lysis induced by cell wall-targeting drugs. The addition of a bead-beating lysis step prior to luminescence measurement abolishes the ATP burst, enabling a more reliable assessment of intracellular ATP levels with this assay. Our findings thus establish a direct link between the ATP burst and the canonical mechanism of action of cell wall inhibitors. We further demonstrate the utility of this approach as a functional readout for identifying compounds that disrupt the mycobacterial cell wall and for screening synergistic or antagonistic interactions with known cell wall-targeting agents. Together, our results elucidate the mechanistic basis of the ATP burst and provide a valuable tool for antimycobacterial drug discovery and development.

microbiology↗

bioRxiv2024

Establishing the foundations for a data-centric AI approach for virtual drug screening through a systematic assessment of the properties of chemical data

Researchers have adopted model-centric artificial intelligence (AI) approaches in cheminformatics by using newer, more sophisticated AI methods to take advantage of growing chemical libraries. It has been shown that complex deep learning methods outperform conventional machine learning (ML) methods in QSAR and ligand-based virtual screening1-3 but such approaches generally lack explanability. Hence, instead of developing more sophisticated AI methods (i.e., pursuing a model-centric approach), we wanted to explore the potential of a data-centric AI paradigm for virtual screening. A data-centric AI is an intelligent system that would automatically identify the right type of data to collect, clean and curate for later use by a predictive AI and this is required given the large volumes of chemical data that exist in chemical databases - PubChem alone has over 100 million unique compounds. However, a systematic assessment of the attributes and properties of suitable data is needed. We show here that it is not the result of deficiencies in current AI algorithms but rather, poor understanding and erroneous use of chemical data that ultimately leads to poor predictive performance. Using a new benchmark dataset of BRAF ligands that we developed, we show that our best performing predictive model can achieve an unprecedented accuracy of 99% with a conventional ML algorithm (SVM) using a merged molecular representation (Extended + ECFP6 fingerprints), far surpassing past performances of virtual screening platforms using sophisticated deep learning methods. Thus, we demonstrate that it is not necessary to resort to the use of sophisticated deep learning algorithms for virtual screening because conventional ML can perform exceptionally well if given the right data and representation. We also show that the common use of decoys for training leads to high false positive rates and its use for testing will result in an over-optimistic estimation of a models predictive performance. Another common practice in virtual screening is defining compounds that are above a certain pharmacological threshold as inactives. Here, we show that the use of these so-called inactive compounds lowers a models sensitivity/recall. Considering that some target proteins have a limited number of known ligands, we wanted to also observe how the size and composition of the training data impact predictive performance. We found that an imbalance training dataset where inactives outnumber actives led to a decrease in recall but an increase in precision, regardless of the model or molecular representation used; and overall, we observed a decrease in the models accuracy. We highlight in this study some of the considerations that one needs to take into account in future development of data-centric AI for CADD.

cancer biology↗

bioRxiv2023

A novel triptolide analog downregulates NF-κB and induces mitochondrial apoptosis pathways in human pancreatic cancer

BackgroundPancreatic cancer is the seventh leading cause of cancer-related death worldwide, and despite advancements in disease management, the 5-year survival rates stands at only 9%. Triptolides have potent anti-tumor activity against different types of cancers, including pancreatic cancer, however poor solubility and toxicity limit their translation into clinical use. MethodsWe synthesized a novel pro-drug of triptolide, (E)-19-[(1-benzoyloxy-1-phenyl)-methylidene]-Triptolide (CK21), and formulated into an emulsion for in vitro and in vivo testing in rats and mice, and using human pancreatic cancer cell lines and patient-derived pancreatic tumor organoids. A time-course transcriptomic profiling of tumor organoids treated with CK21 in vitro was conducted to define its mechanism of action, as well as transcriptomic profiling at a single time point post-CK21 administration in vivo. FindingsIntravenous administration of emulsified CK21 resulted in the stable release of triptolide, and potent anti-proliferative effects on human pancreatic cancer cell lines and patient-derived pancreatic tumor organoids in vitro, and with minimal toxicity in vivo. Time course transcriptomic profiling of tumor organoids treated with CK21 in vitro revealed <10 differentially expressed genes (DEGs) at 3 h and [~]8,000 DEGs at 12 h. Overall inhibition of general RNA transcription was observed, and Ingenuity pathway analysis together with functional cellular assays confirmed inhibition of the NF-{kappa}B pathway, increased oxidative phosphorylation and mitochondrial dysfunction, leading ultimately to increased reactive oxygen species (ROS) production, reduced B-cell-lymphoma protein 2 (BCL2) expression, and mitochondrial-mediated tumor cell apoptosis. InterpretationCK21 is a novel pro-drug of triptolide that exerts potent anti-proliferative effects on human pancreatic tumors by inhibiting the NF-{kappa}B pathway, leading ultimately to mitochondrial-mediated tumor cell apoptosis. FundingThe study of the anti-tumor efficacy of CK21 supported in part by a research grant from Cinkate Pharmaceutical Corp; the funders had no role in the study design, interpretation or decision to publish. Patient-derived pancreatic tumor organoids were a generous gift from the Organoid and Primary Culture Research Core at University of Chicago.

pharmacology and toxicology↗

bioRxiv2022

Microtubule-Connexin-43 regulation suppresses arrhythmias and fibrosis in Duchenne muscular dystrophy mice.

Dilated cardiomyopathy is the leading cause of death in Duchenne muscular dystrophy (DMD) patients due to advancements in skeletal muscle therapies yet limited presence of cardiac treatments. The phosphorylation status of gap junction protein Connexin-43 (Cx43) drives Cx43 remodeling and the development of arrhythmias and fibrosis. Based on evidence that Colchicine drug treatment improves Cx43 phosphorylation and remodeling, we compared the microtubule cytoskeleton in DMD mice (mdx) versus mdx mice genetically altered to be Cx43-phosphorylation-deficient (mdxS3A). Reciprocally, we analyzed the microtubule cytoskeleton in mdx mice genetically altered to be Cx43-phospho-mimicking (mdxS3E). We found a link between the phospho-status of Connexin-43 and regulation of microtubule organization, in which phospho-dead Cx43 (S3A) inhibits improvements seen with Colchicine treatment in mdx mice, and phospho-mimic S3E promotes microtubule reorganization in mdx mice. A reduction in arrhythmias and fibrosis suggests an unsuspecting Cx43-microtubule link for translational corrective activities for DMD cardiomyopathy.

cell biology↗

bioRxiv2021

Molecular Pathophysiology of Cardiac Injury and Cardiac Microthrombi in Fatal COVID-19: Insights from Clinico-histopathologic and Single Nuclei RNA Sequencing Analyses

Cardiac injury is associated with critical COVID-19, yet its etiology remains debated. To elucidate the pathogenic mechanisms of COVID-19-associated cardiac injury, we conducted a single-center prospective cohort study of 69 COVID-19 decedents. Of six cardiac histopathologic features, microthrombi was the most commonly detected (n=48, 70%). We tested associations of cardiac microthrombi with biomarkers of inflammation, cardiac injury, and fibrinolysis and with in-hospital antiplatelet therapy, therapeutic anticoagulation, and corticosteroid treatment, while adjusting for multiple clinical factors, including COVID-19 therapies. Higher peak ESR and CRP during hospitalization were independently associated with higher odds of microthrombi. Using single nuclei RNA-sequence analysis, we discovered an enrichment of pro-thrombotic/anti-fibrinolytic, extracellular matrix remodeling, and immune-potentiating signaling amongst cardiac fibroblasts in microthrombi-positive COVID-19 hearts relative to microthrombi-negative COVID-19. Non-COVID-19 non-failing hearts were used as reference controls. Our cumulative findings identify the specific transcriptomic changes in cardiac fibroblasts as salient features of COVID-19-associated cardiac microthrombi.

pathology↗

bioRxiv2021

A scalable, multi-wavelength, broad bandwidth frequency-domain near-infrared spectroscopy platform for real-time quantitative tissue optical imaging

Frequency-domain near-infrared spectroscopy (FD-NIRS) provides quantitative noninvasive measurements of tissue optical absorption and scattering, and provides a safe and accurate method for characterizing tissue composition and metabolism. However, the poor scalability and high complexity of most FD-NIRS systems assembled to date have contributed to its limited clinical impact. To address these shortcomings, we present a scalable, digital-based FD-NIRS platform capable of measuring optical properties and tissue chromophore concentrations in real-time. The system provides single-channel FD-NIRS amplitude/phase, optical property, and chromophore data at a maximum display rate of 36.6 kHz, 17.9 kHz, and 10.2 kHz, respectively, and can be scaled to multiple channels as well as integrated into a handheld format. The entire system is enabled by several innovations including an ultra-high-speed k-nearest neighbor lookup table method (maximum of 250,000 inversions/s for large 2500x700 table of absorption and reduced scattering coefficients), embedded FPGA and CPU high-speed co-processing, and high-speed data transfer (due to on-board processing). We show that our 6-wavelength, broad modulation bandwidth (1-400 MHz) system can be used to perform 2D high-density spatial mapping of optical properties.

bioengineering↗

bioRxiv2021

O-GlcNAcylation reduces phase separation and aggregation of the EWS N-terminal low complexity region

Many membraneless organelles are thought to be biomolecular condensates formed by phase separation of proteins and other biopolymers. Post-translational modifications (PTMs) can impact protein phase separation behavior, although for many PTMs this aspect of their function is unknown. O-linked {beta}-D-N-acetylglucosaminylation (O-GlcNAcylation) is an abundant form of intracellular glycosylation whose roles in regulating biomolecular condensate assembly and dynamics have not been delineated. Using an in vitro approach, we found that O-GlcNAcylation reduces the phase separation propensity of the EWS N-terminal low complexity region (LCRN) under different conditions, including in the presence of the arginine-and glycine-rich RNA-binding domains (RBD). O-GlcNAcylation enhances fluorescence recovery after photobleaching (FRAP) within EWS LCRN condensates and causes the droplets to exhibit more liquid-like relaxation following fusion. Following extended incubation times, EWS LCRN+RBD condensates exhibit diminished FRAP, indicating a loss of fluidity, while condensates containing the O-GlcNAcylated LCRN do not. In HeLa cells, EWS is less O-GlcNAcylated following OGT knockdown and more prone to aggregation based on a filter retardation assay. Relative to the human proteome, O-GlcNAcylated proteins are enriched with regions that are predicted to phase separate, suggesting a general role of O-GlcNAcylation in regulation of biomolecular condensates. Insert Table of Contents artwork here O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=136 SRC="FIGDIR/small/443654v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@a09fb6org.highwire.dtl.DTLVardef@1556f47org.highwire.dtl.DTLVardef@1fcd76borg.highwire.dtl.DTLVardef@a2dbda_HPS_FORMAT_FIGEXP M_FIG C_FIG For Table of Contents only.

biochemistry↗

bioRxiv2019

The Creative Mind: Blending Oxytocinergic, Dopaminergic and Personality

In a fast-changing world, creative thinking (CT) is an extraordinary currency. Oxytocin (OT) is associated with CT and release of OT depends on ADP ribosyl-cyclases (CD38 and CD157). Moreover, CT as well as OTs mechanism of action are mediated via central dopaminergic pathways. Consequently, we evaluate the roles of CD38, CD157, dopamine receptor D2 (DRD2) and catechol-O-methyltransferase (COMT) peripheral gene expression in CT. Two principal domains of CT, divergent thinking and insight solving problems, were assessed using validated behavioral assessments. To facilitate discriminant validity, two established correlates of CT, trait Openness and fluid intelligence as well as age and sex were included in the regression model. In women, significant main effects (p<0.01) were positively associated with the expression CD38, CD15, and their interaction CD38 x CD157 controlling for Openness, fluid intelligence and age. Subsequent analysis on the subscale-level revealed significant main effects for CD157 and CD38 x CD157 in men specifically for divergent thinking. In women, significant (p<0.01) results are also observed for dopaminergic expression (DRD2, COMT, DRD2 x COMT). The full model (oxytocinergic and dopaminergic gene expressions, Openness, and fluid intelligence) explains a sizable 39% of the variance in females. Significant main effects are observed for CD38, CD157, DRD2 and COMT as well as their interactions (CD38xCD157 and DRD2xCOMT). In conclusion, we show that oxytocinergic and dopaminergic gene expression contribute significantly to the complex CT phenotype suggesting the notion that the perspective gained from examining the peripheral transcriptome meaningfully adds to understanding the landscape of creative thinking.\n\nSignificance StatementCreative thinking (CT) is a powerful driving force galvanizing progress and civilization. Towards better understanding the neurobiology of CT, we implement a gene expression strategy that is considered to capture not only genomic elements but also environmental signatures. We employ laboratory measures of CT (alternative uses test and insight problem solving), controlling for fluid intelligence and the personality trait of Openness. We focus on oxytocinergic and dopaminergic genes that contribute to the molecular architecture of CT. Oxytocinergic and dopaminergic gene expression significantly explains a robust 39% of the variance in CT. Notably, this study demonstrates the potential of the peripheral transcriptome towards tracing gene pathways underlying some complex cognitive behaviors such as creative thinking.

neuroscience↗

bioRxiv2016

Generation of heritable germline mutations in the jewel wasp Nasonia vitri pennis using CRISPR/Cas9

The revolutionary RNA-guided endonuclease CRISPR/Cas9 system has proven to be a powerful tool for gene editing in a plethora of organisms. Here, utilizing this system we developed an efficient protocol for the generation of heritable germline mutations in the parasitoid jewel wasp, Nasonia vitripennis, a rising insect model organism for the study of evolution, development of axis pattern formation, venom production, haplo-diploid sex determination, and host-symbiont interactions. To establish CRISPR-directed gene editing in N. vitripennis, we targeted a conserved eye pigmentation gene cinnabar, generating several independent heritable germline mutations in this gene. Briefly, to generate these mutants, we developed a protocol to efficiently collect N. vitripennis eggs from a parasitized flesh fly pupa, Sarcophaga bullata, inject these eggs with Cas9/guide RNA mixtures, and transfer injected eggs back into the host to continue development. We also describe a flow for screening mutants and establishing stable mutant strains through genetic crosses. Overall, our results demonstrate that the CRISPR/Cas9 system is a powerful tool for genome manipulation in N. vitripennis, with strong potential for expansion to target critical genes, thus allowing for the investigation of a number of important biological phenomena in this organism.

molecular biology↗